Origin of the large phonon band-gap in SrTiO3 and the vibrational signatures of ferroelectricity in ATiO3 perovskite: First principles lattice dynamics and inelastic neutron scattering of PbTiO3, BaTiO3 and SrTiO3

We report first principles density functional perturbation theory calculations and inelastic neutron scattering measurements of the phonon density of states, dispersion relations and electromechanical response of PbTiO3, BaTiO3 and SrTiO3. The phonon density-of-states of the quantum paraelectric SrTiO3 is found to be fundamentally distinct from that of ferroelectric PbTiO3 and BaTiO3 with a large 70-90 meV phonon band-gap. The phonon dispersion and electromechanical response of PbTiO3 reveal giant anisotropies. The interplay of covalent bonding and ferroelectricity, strongly modulates the electromechanical response and give rise to spectacular signatures in the phonon spectra. The computed charge densities have been used to study the bonding in these perovskites. Distinct bonding characteristics in the ferroelectric and paraelectric phases give rise to spectacular vibrational signatures. While a large phonon band-gap in ATiO3 perovskites seems a characteristic of quantum paraelectrics, anisotropy of the phonon spectra correlates well with ferroelectric strength. These correlations between the phonon spectra and ferroelectricity, can guide future efforts at custom designing still more effective piezoelectrics for applications. These results suggest that vibrational spectroscopy can help design novel materials.Comment: 11 pages, 4 color figures and 2 Table

Wnt4 and LAP2alpha as pacemakers of Thymic Epithelial Senescence

Age-associated thymic involution has considerable physiological impact by inhibiting de novo T-cell selection. This impaired T-cell production leads to weakened immune responses. Yet the molecular mechanisms of thymic stromal adipose involution are not clear. Age-related alterations also occur in the murine thymus providing an excellent model system. In the present work structural and molecular changes of the murine thymic stroma were investigated during aging. We show that thymic epithelial senescence correlates with significant destruction of epithelial network followed by adipose involution. We also show in purified thymic epithelial cells the age-related down-regulation of Wnt4 (and subsequently FoxN1), and the prominent increase in LAP2α expression. These senescence-related changes of gene expression are strikingly similar to those observed during mesenchymal to pre-adipocyte differentiation of fibroblast cells suggesting similar molecular background in epithelial cells. For molecular level proof-of-principle stable LAP2α and Wnt4-over-expressing thymic epithelial cell lines were established. LAP2α over-expression provoked a surge of PPARγ expression, a transcription factor expressed in pre-adipocytes. In contrast, additional Wnt4 decreased the mRNA level of ADRP, a target gene of PPARγ. Murine embryonic thymic lobes have also been transfected with LAP2α- or Wnt4-encoding lentiviral vectors. As expected LAP2α over-expression increased, while additional Wnt4 secretion suppressed PPARγ expression. Based on these pioneer experiments we propose that decreased Wnt activity and increased LAP2α expression provide the molecular basis during thymic senescence. We suggest that these molecular changes trigger thymic epithelial senescence accompanied by adipose involution. This process may either occur directly where epithelium can trans-differentiate into pre-adipocytes; or indirectly where first epithelial to mesenchymal transition (EMT) occurs followed by subsequent pre-adipocyte differentiation. The latter version fits better with literature data and is supported by the observed histological and molecular level changes

Application of Ontology Translation

Abstract. An ontology provides a precise specification of the vocabulary used by a community of interest (COI). Multiple communities of interest may describe the same concept using the same or different terms. When such communities interact, ontology alignment and translation is required. This is typically a time consuming process. This paper describes Snoggle, an open source tool designed to ease development of ontology translation rules, and discusses its application to geospatial ontologies

Reduced Expression of Ribosomal Proteins Relieves MicroRNA-Mediated Repression

MicroRNAs (miRNAs) regulate physiological and pathological processes by inducing posttranscriptional repression of target messenger RNAs (mRNAs) via incompletely understood mechanisms. To discover factors required for human miRNA activity, we performed an RNAi screen using a reporter cell line of miRNA-mediated repression of translation initiation. We report that reduced expression of ribosomal protein genes (RPGs) dissociated miRNA complexes from target mRNAs, leading to increased polysome association, translation, and stability of miRNA-targeted mRNAs relative to untargeted mRNAs. RNA sequencing of polysomes indicated substantial overlap in sets of genes exhibiting increased or decreased polysomal association after Argonaute or RPG knockdowns, suggesting similarity in affected pathways. miRNA profiling of monosomes and polysomes demonstrated that miRNAs cosediment with ribosomes. RPG knockdowns decreased miRNAs in monosomes and increased their target mRNAs in polysomes. Our data show that most miRNAs repress translation and that the levels of RPGs modulate miRNA-mediated repression of translation initiation.W. M. Keck Foundation (Distinguished Young Scholars Award